More than 650 million tons/year of fluvial sediment are delivered from continental regions into the South China Sea (SCS). Previous studies have shown that the composition of the magnetic fraction of riverine sediments drained into the SCS is significantly variable from north to south. On the basis of this evidence, we now examine a full set of magnetic properties for a number of core‐tops taken at water depth comprised mostly between 800 and 3500 m. Room‐temperature magnetic parameters and thermal spectra are used to obtain information about the concentration and mineralogical magnetic composition. Spatial changes are observed in the relative proportion of magnetite and hematite with an increase of the latter toward the south, similarly to the observation on land. However, the N‐S contrast is much weaker in marine core tops than in river sediments, because of the role played by the shelf in partly trapping river‐borne sediments, in particular in the southern SCS. In part, sediments also reach the continental slope and the deep basins, being transported and mixed by surface and deep‐water currents, which yield the magnetite‐hematite mixing in the south. For the first time, we characterize a wide spectrum of magnetic properties of modern marine sediment in the South China Sea. Our results give important insights into the modern pathways of sediment particles, depicting the source‐to‐sink processes that affect the terrigenous sediment load.